Yue Chen, PhD

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Personal Statement

Exploring the mechanism of HCV spontaneous clearance in HIV-1 infected individuals. For some unclear reasons, HCV infections are spontaneously cleared in certain HIV/HCV coinfected individuals, whereas in majority of HIV/HCV coinfected individuals, HCV infections progress to chronicity. To explore the mechanism of such difference, plasma RNA from HIV-1 infected subjects with HCV spontaneous clearance or chronic infection have being comprehensively analyzed following next generation sequencing of plasma RNA to elucidate the mechanism of HCV spontaneous clearance.

--- Exploring the role of oral microbiome in HIV pathogenesis. Human oral cavity is home to several million bacteria. The oral microbiome is particularly important to health because it can cause both oral and systemic disease. Oral microbiota in HIV infected individuals plays an important role in initiation and/or enhancement of oral infections. Furthermore, HIV infects oral mucosal tissues and dysregulates oral microbiome. HIV-associated periodontal diseases could lead to microbial translocation and serve as a source of chronic and systemic immune activation, which increases the risk of cardiovascular diseases and pulmonary diseases.
--In cancer patients, tumor cells are rapidly dividing, constantly releasing tumor DNA into the blood. Recent advances in next-generation sequencing have made it possible to sequence circulating tumor DNA (ctDNA) in blood plasma with high sensitivity and specificity, termed “liquid biopsy”. This will have a key role in clinically assisting early diagnosis, longitudinal analyses of tumor evolution and personalized therapeutic intervention. We hypothesize that there are sufficient ctDNA in the plasma of HIV-1 infected MACS subjects at least 6 months prior to development of AIDS- associated cancers that can be measured and used as biomarkers for early diagnosis and personalized therapeutic intervention of AIDS related cancers. To detect the ctDNA in plasma samples of AIDS- associated cancer patients before and after the cancer diagnosis, longitudinal MACS plasma samples are being used to detect ctDNA via a next-generation sequencing with an Ion AmpliSeq comprehensive cancer panel, which targets 409 tumor suppressor genes and oncogenes frequently cited and frequently mutated in cancer cells. The quantity and evolution of ctDNA will be monitored in plasma DNA. Our eventual goal is to develop a noninvasive method for detecting plasma ctDNA, which assists early diagnosis and personalized therapeutic intervention for AIDS- associated cancers.